Abstract 2061: Protein network analysis uncovers a poor-survival subtype in multiple myeloma
Authors: Anish K. Simhal, Kylee H. Maclachlan, Rena Elkin, Jiening Zhu, Saad Z. Usmani, Jonathan J. Keats, Larry Norton, Joseph O. Deasy, Jung Hun Oh, Allen Tannenbaum
Journal: Cancer Research (2023)

Abstract Multiple myeloma (MM) prognosis incorporates a variety of metrics including treatment received, clinical factors, and genomic characteristics, with several specific genomic features predicting for shorter progression free survival (PFS). No study to date has integrated genomic data from a systems view, incorporating interactions between biomarkers in a network. We use a geometric network analysis that integrates complex interactions to characterize patterns of biological behavior not captured by individual genomic events. The methodology is mathematically well-defined and has no fitting parameters. We hypothesized that such a systems mathematical approach applied to gene interaction networks may delineate biologically relevant MM subtypes and potential new therapeutic targets. We overlaid RNA-Seq and copy number alteration data from the MMRF CoMMpass study (IA19) on a gene interactome derived from the Human Protein Reference Database using a novel graph metric of network robustness — Ollivier-Ricci curvature (ORC). Results were clustered, with the optimal number determined via silhouette score. Survival analysis for PFS was performed employing Kaplan-Meier and log-rank tests. A differential gene expression analysis between high and low risk groups was conducted. Differences in scalar ORC between the low-risk and high-risk groups were examined and contextualized using a pathway analysis. Pathway analysis was performed using the Broad Institute’s Gene Set Enrichment Analysis tool and the pathways used are from the hallmark gene set from the Human MSigDB collection. The dataset included 659 patients and the incorporated protein-protein interactions resulted in a network with 8,468 nodes and 33,695 edges. The ORC analysis discovered 6 clusters, with specific genomic features being associated with clusters predicting for long [hyperdiploidy, t(11:14)], and short [t(4;14), MAF/MAFB translocations] PFS. A differential gene expression analysis comparing the high risk and low risk groups identified 118 key genes. These genes were associated with various pathways both known and unknown to be associated with multiple myeloma, including mitotic spindle, DNA repair, inflammatory response, and the P53 pathways. Further scalar curvature analysis showed differences in the apoptosis, TGF beta signaling, and other signaling pathways. In summary, we applied the geometric network analysis tool ORC to multi-omics data in MM represented as biological networks to identify individuals at high risk of short PFS and relevant biological correlates. Decreased robustness of signaling near immune-related genes was associated with shorter survival, highlighting the plausible utility of using these methods to uncover new biological insights. Citation Format: Anish K. Simhal, Kylee H. Maclachlan, Rena Elkin, Jiening Zhu, Saad Z. Usmani, Jonathan J. Keats, Larry Norton, Joseph O. Deasy, Jung Hun Oh, Allen Tannenbaum. Protein network analysis uncovers a poor-survival subtype in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2061.